Chemical modeling apparatus

ABSTRACT

The present invention relates to an apparatus for modeling chemical structures having multiple types of bonding. In an embodiment, the present invention relates to an apparatus for modeling chemical structures having multiple types of bonding, including hydrogen bonding. In an embodiment, the invention is a molecular modeling device including a plurality of molecular components. The molecular components can include a first elemental component comprising a plurality of first magnets, a second elemental component comprising a second magnet, and a primary structural bond attaching the first elemental component to the second elemental component. The molecular components can be attached to other molecular components through secondary structural bonds, wherein the primary structural bond attaches more strongly than the secondary structural bond. In an embodiment, the first and second magnets each include first and second magnetic poles, the first magnets disposed on the exterior of the first elemental component with the first magnetic pole pointing away from the interior of the first elemental components. The second magnet can be disposed on the exterior of the second elemental component with the second magnetic pole of the second magnet pointing away from the interior of the second elemental component.

FIELD OF THE INVENTION

The present invention relates to an apparatus for modeling chemicalstructures. More specifically, the present invention relates to anapparatus for modeling chemical structures having multiple types ofbonding.

BACKGROUND OF THE INVENTION

Atoms are the building blocks of all matter. Atoms can associate withother atoms through chemical bonds. A chemical bond can be said to existbetween two atoms or groups of atoms when forces acting between themlead to the formation of an aggregate with sufficient stability to makeit convenient for the scientist to consider it as an independentmolecular species. See L. Pauling, 1960, The Nature of the ChemicalBond. Understanding the effect that chemical bonding has on molecularstructure is important in many areas of study including chemistry,physics, and biology.

Chemical bonds can be broadly classified as electrostatic, covalent, andmetallic. More specific classifications of bonding can be made underthese three broad categories. By way of example, ionic bonds, ion-dipolebonds, and hydrogen bonds can all be thought of as electrostatic bonds,in whole or in part.

Various modeling systems for chemical structures and bonding exist. Byway of example, U.S. Pat. No. 6,508,652 (Kestyn) and U.S. Pat. No.4,099,339 (Snelson) disclose chemical modeling systems. These modelingsystems can help in visualizing the structure of chemical compounds.However, such modeling systems do not allow one to visualize the effectthat hydrogen bonding has on the structure of molecules or on howmolecules are arranged with respect to one another. Also, such modelingsystems do not allow one to see the structural effects of differenttypes of bonding having different relative strengths, such as thedifference in strength between covalent bonding and ion-dipole bonding.

Therefore, a need exists for a chemical modeling system that will modelthe effects of hydrogen bonding and/or ion-dipole bonding.

SUMMARY OF THE INVENTION

The present invention relates to an apparatus for modeling chemicalstructures having multiple types of bonding, including ion-dipolebonding and/or dipole-dipole bonding including hydrogen bonding. In anembodiment, the invention is a molecular modeling device including aplurality of molecular components including a first elemental componentcomprising a plurality of first magnets and a second elemental componentcomprising a second magnet. A primary structural bond can attach thefirst elemental component to the second elemental component. In anembodiment, the primary structural bond can model a covalent bond. Themolecular components can be attached to other molecular componentsthrough secondary structural bonds, wherein the primary structural bondattaches more strongly than the secondary structural bond. In anembodiment, the secondary structural bond models an ion-dipole bond. Inan embodiment, the secondary structural bond models a dipole-dipolebond. In an embodiment the secondary structural bond models a hydrogenbond. In an embodiment, the first and second magnets each include firstand second magnetic poles. The first magnets can be disposed on theexterior of the first elemental component with the first magnetic polepointing away from the interior of the first elemental components. Thesecond magnet can be disposed on the exterior of the second elementalcomponent with the second magnetic pole of the second magnet pointingaway from the interior of the second elemental component.

In an embodiment, the invention is directed to a molecular modelingdevice comprising a plurality of molecular components comprising a firstatomic component and a second atomic component and means for attachingmolecular components together to simulate both primary and secondarystructure of a chemical compound.

The above summary of the present invention is not intended to describeeach discussed embodiment of the present invention. This is the purposeof the figures and the detailed description that follows.

DRAWINGS

The invention may be more completely understood in connection with thefollowing drawings, in which:

FIG. 1 is a front schematic view of a modeling component in accordancewith an embodiment of the invention modeling water (H₂O).

FIG. 2 is a back schematic view of the modeling component of FIG. 1.

FIG. 3 is a cross-sectional schematic view of a modeling component takenalong lines A-A′ of FIG. 1.

FIG. 4 is a cross-sectional schematic view of the modeling componenttaken along lines B-B′ of FIG. 2.

FIG. 5 is a cross-sectional schematic view of an alternative embodimentof a modeling component.

FIG. 6 is cross-section schematic view of a modeling component withmagnets that are disposed within channels away from the surface of themodeling component.

FIG. 7 is a schematic view of another embodiment of a modeling componentin accordance with the invention.

FIG. 8 is a schematic side offset view of another embodiment of amodeling component in accordance with the invention.

FIG. 9 is a schematic view of an embodiment of the invention modeling ahydrogen-bonded cyclic five-water complex.

FIG. 10 is a schematic view of an embodiment of the invention modeling ahydrogen bonded cyclic six-water complex (primitive unit cell ofhexagonal ice).

FIG. 11 is a schematic offset view of an embodiment of the inventionmodeling two hexagonal water complexes hydrogen bonded to each other(complete unit cell of hexagonal ice).

FIG. 12A is a schematic view of an embodiment of the invention modelinga hydroxyl ion, shown along with a model of a water molecule.

FIG. 12B is a schematic view of an embodiment of the invention modelinga hydrated hydroxyl ion, H₃O₂ ⁻.

FIG. 13A is schematic view of an embodiment of the invention modelingthe formation of a hydronium ion, shown along with models of three watermolecules that can hydrate the hydronium ion.

FIG. 13B is a schematic view of an embodiment of the invention modelinga hydrated hydronium ion, H₉O₄ ⁺.

While the invention is susceptible to various modifications andalternative forms, specifics thereof have been shown by way of exampleand drawings, and will be described in detail. It should be understood,however, that the invention is not limited to the particular embodimentsdescribed. On the contrary, the intention is to cover modifications,equivalents, and alternatives falling within the spirit and scope of theinvention.

DETAILED DESCRIPTION OF THE INVENTION

As described more fully below, chemical bonds can broadly be classifiedinto three main types: electrostatic, covalent, and metallic.Electrostatic bonds include ion-dipole bonds and dipole-dipole bonds,including hydrogen bonding. Ion-dipole bonding is an attractive forcebetween an atom or molecule having a charge and an atom or moleculehaving a region(s) of greater or lesser electron density. An examplewould be the solvation of a sodium ion by a plurality of watermolecules. Hydrogen bonding is a species of dipole-dipole bonding andcan be described as an attractive force between opposite charges,molecules arising from the attraction between regions of greaterelectron density and regions of lesser electron density. Hydrogenbonding affects the structure of both molecules and complexes ofmolecules. By way of example, hydrogen bonding between water moleculesaffects the structure that complexes of water molecules take on, in bothliquid and solid forms.

Both ion-dipole bonding and dipole-dipole bonding have an enormousamount of significance in understanding the structural forms assumed bymolecules. In the context of biochemistry, hydrogen bonding directlyaffects the structure of macromolecules such as proteins. In turn, thefunction of a protein depends on its three-dimensional structure. Forexample, the catalytic activity of an enzyme depends on itsthree-dimensional structure. Beyond its native conformation, a givenpolypeptide chain can theoretically assume countless differentstructural conformations. However, the native conformation of apolypeptide chain is stabilized and can be favored, in part, by hydrogenbonding. Therefore, by way of example, understanding how hydrogenbonding affects molecular structure is important to understanding thestructure and function of proteins.

The present invention relates to an apparatus for modeling chemicalstructures having multiple types of bonding, including ion-dipolebonding and/or dipole-dipole bonding such as hydrogen bonding. By way ofexample, the applicant has discovered that the effects of ion-dipolebonding and/or dipole-dipole can be modeled using components includingmagnets to simulate areas of greater or lesser electron density on anatom or molecule. In an embodiment, the invention is a molecularmodeling device including a plurality of molecular components includinga first elemental component comprising a plurality of first magnets anda second elemental component comprising a second magnet. A primarystructural bond can attach the first elemental component to the secondelemental component. In an embodiment, the primary structural bond canmodel a covalent bond. The molecular components can be attached to othermolecular components through secondary structural bonds, wherein theprimary structural bond attaches more strongly than the secondarystructural bond. In an embodiment, the secondary structural bond modelsan ion-dipole bond. In an embodiment, the secondary structural bondmodels a dipole-dipole bond. In an embodiment the secondary structuralbond models a hydrogen bond. In an embodiment, the first and secondmagnets each include first and second magnetic poles. The first magnetscan be disposed on the exterior of the first elemental component withthe first magnetic pole pointing away from the interior of the firstelemental components. The second magnet can be disposed on the exteriorof the second elemental component with the second magnetic pole of thesecond magnet pointing away from the interior of the second elementalcomponent.

Chemical Bonding

Chemical bonds account for the forces uniting atoms into molecules,giving symmetry and order to substances of incredible variety anddesign. Linus Pauling's monograph, The Nature of the Chemical Bond,(©1938, 1940, and 1960) is a principal reference in this field,providing perspective important in many scientific fields today.

According to Pauling, chemical bonds may be classified into threegeneral categories: electrostatic, covalent, or metallic bonds. Thisorganization is not a rigorous one, for many chemical bonds are mixturesof these limiting arrangements. For example, particular covalent bondshave partial electrostatic or ionic character, including —OH, >CO,or >NH. The ionic character arises from a dissimilarity of atoms bondedtogether, a property Pauling defined as electronegativity.

Pauling's electronegativity index assigns a number to each elementaccording one atom's ability to sequester electrons (charge) from otheratoms bonded to it. For instance, the electronegativity of hydrogen(H)=2.1, carbon (C)=2.5, nitrogen (N)=3.0, and oxygen (O)=3.5. Thedifferences when combined suggests that the carbon-hydrogen bond is notvery ionic Δ(CH)=0.4, the nitrogen-hydrogen bond is moderately ionicΔ(NH)=0.9, and the oxygen-hydrogen bond yet is more ionic Δ(OH)=1.4. Theelectronegativity numbers have no units but are approximate indices forcomparative use.

The consequences of ionic character to chemical bonds are far-ranging.They include (1) increased solubility of ionic solids (salts) in polar(ionic-covalent) solvents such as water (H₂O), and (2) strongintermolecular attraction between molecules of unique orientation,particularly configurations involving a hydrogen atom bridge, thehydrogen bond.

Under certain conditions, an atom of hydrogen is attracted by ratherstrong forces to two atoms (such as oxygen and/or nitrogen), instead ofone, so that the hydrogen may be considered to be acting as a bondbetween them. This is called the hydrogen bond.

The hydrogen bond often is represented by an ellipsis ( . . . ).Examples of a hydrogen bond are: between two water molecules (H₂O . . .HOH) or between two peptide moieties in a protein (O . . . HN).Depending on the bond strength, the inter-atomic distance for a hydrogenbond is larger than that of a covalent OH or NH bond; typically, an O .. . H distance=1.7 Å, whereas the approximate HO covalent bonddistance=1.0 Å. (the Angstrom unit of length=10⁻¹⁰ meters). This bondasymmetry is usually maintained throughout the process of making ahydrogen bond, or of breaking it. Hydrogen bonding can also lead tochemical change that may be instrumental to certain chemical processesor biochemical pathways. Such changes may be visualized in the mind oncea three-dimensional model is held firmly in the hand.

The hydrogen bond typically is secondary in strength to that of itscovalent partner. The energy to dissociate a hydrogen bond in water isabout five percent of a primary O—H covalent bond, but the energy isimportant, indeed vital, to the function of water as a high-densityliquid, having a large heat capacity and heat of vaporization, a highdielectric constant and large surface tension. The hydrogen bond also isa directed bond, imposing structure to what otherwise may be a chaoticmixture.

The example of a water molecule includes two hydrogen atoms having, onaverage, a net positive charge. In turn, the oxygen atom has, onaverage, two negative charges on the opposite side of the molecule fromthe two hydrogen atoms. The two negative charges are somewhat diffusebut generally positioned 109 degrees apart. Thus, water moleculesgenerally require preferential orientation to engage in hydrogenbonding.

As stated above, embodiments of the present invention relate to anapparatus for modeling chemical structures having multiple types ofbonding, including ion-dipole bonding and/or dipole-dipole bondingincluding hydrogen bonding. While not limiting the scope of the presentinvention, exemplary modeling apparatus structures will now bedescribed.

Modeling Apparatus

Referring to FIG. 1, a front schematic view of a modeling component 10in accordance with an embodiment of the invention is shown. A firstelemental component 1 is shown attached to two second elementalcomponents 3, 7. In this view, first elemental component 1 is shown as asphere. However, one of skill in the art will appreciate that firstelemental component 1 could be made in other shapes. In an embodiment,portions of the sphere are flattened to create an irregular sphere. Byway of example, in an embodiment, portions of the sphere where firstelemental component 1 is attached to two second elemental components 3,7 can be flattened so that the sphere of the first element and thespheres of the second elemental components intersect. Both of the secondelemental components 3, 7, have a magnet 5, 9, disposed on theirsurface. Magnets 5, 9, may be attached with a screw, a nail, anadhesive, or the like. By way of example, magnet 5 may be attached tosecond elemental component 3 with an adhesive. The magnets 5, 9, aredisposed on second elemental components 3, 7, so as to reflect positionsof lesser electron density, net positive charge on the atom. In thisview, the North pole of the magnets 5, 9, is shown pointing away fromthe first elemental component 1. Referring now to FIG. 2, a backschematic view of the modeling component 10 of FIG. 1 is shown. Magnets11, 13 are disposed on the surface of first elemental component 1.Magnets 11, 13, may be attached with a screw, a nail, an adhesive, orthe like. By way of example, magnet 11 may be attached to secondelemental component 7 with an adhesive. In this view, the South pole ofthe magnets 11, 13, is shown pointing away from the first elementalcomponent 1.

First elemental component 1 may be made from any of a variety ofmaterials. By way of example, first elemental component 1 may includewood, cellulose fiber, polymer, glass, metal, or a composite material.Second elemental components 3, 7, may also be made from any of a varietyof materials. By way of example, second elemental components 3, 7, mayinclude wood, cellulose fiber, polymer, glass, metal, or a compositematerial.

Referring now to FIG. 3, a cross-sectional schematic view of a modelingcomponent taken along lines A-A′ of FIG. 1 is shown. In this view,fastening device 15 can be seen attaching second elemental component 3to first elemental component 1. Fastening device 17 can be seenattaching second elemental component 7 to first elemental component 1.Fastening devices 15 and 17 may be the same or different. Fasteningdevices 15, 17, may include wood, cellulose fiber, polymer, glass,metal, or a composite. Fastening device 15, 17, may include a screw,such as a wood screw, a nail, a dowel, an adhesive, and the like.Fastening devices may also include threaded protrusions or threadedchannels. By way of example, one elemental component may include aprotrusion having threads adapted and configured to fit withcorresponding threads disposed in a channel on a second elementalcomponent. In this view, the bond angle 19 between lines drawn throughthe center of second elemental components 3, 7, and the center 21 of thefirst elemental component 1 is determined from literature of chemicalbonds and valance. In the case of water ice, the angle 19 isapproximately 109.5 degrees. In an embodiment, the angle 19 may bebetween 100 and 115 degrees. FIG. 3 also shows magnets 5, 9, disposed onsecond elemental components 3, 7. In this view magnets 5, 9, fit into arecessed portion of second elemental components 3, 7. However, magnets5, 9, may also be attached to second elemental components 3, 7, withoutbeing in a recessed portion. Magnets 5, 9, may be attached to secondelemental components 3, 7, with a screw, a nail, an adhesive, and thelike. By way of example, in an embodiment, magnet 5 is attached tosecond elemental component 3 with an adhesive.

Referring now to FIG. 4, a cross-sectional schematic view of a modelingcomponent taken along lines B-B′ of FIG. 2 is shown. In this view, theangle 23 between lines drawn through the center of magnets 11, 13, andthe center 21 of the first elemental component 1 is determined fromliterature of chemical bonds and valance. In the case of water ice, theangle 19 is approximately 109.5 degrees. In an embodiment, the angle 23may be between 100 and 115 degrees. FIG. 4 shows magnets 11, 13,disposed on first elemental component 1. In this view, magnets 11, 13,fit into recessed portions of first elemental component 1. However,magnets 11, 13, may also be attached to first elemental component 1,without being in a recessed portion. Magnets 11, 13, may be attached tofirst elemental component 1, with a screw, a nail, an adhesive, and thelike. By way of example, in an embodiment, magnet 11 is attached tofirst elemental component 1 with an adhesive.

Referring now to FIG. 5, a cross-sectional schematic view of analternative embodiment of a modeling component 50 is shown. Secondelemental component 7 is reversibly attached to first elementalcomponent through attraction between magnet 25 and magnet 27. In thismanner, the modeling system can simulate a hydroxyl ion (OH⁻) whensecond elemental component 7 is not attached to first elementalcomponent 1. The unattached second elemental component 7 can thenassociate with and attach to a model of a water molecule as in FIG. 1 tosimulate a hydronium ion (H₃O⁺) as shown in FIG. 8. Fastening device 15attaches second elemental component 3 to first elemental component 1.Fastening device 15 may include wood, cellulose fiber, polymer, glass,metal, or a composite. Fastening device 15 may include a screw, such asa wood screw, a nail, a dowel, an adhesive, and the like. In this view,the angle 19 between lines drawn through the center of second elementalcomponents 3, 7, and the center 21 of the first elemental component 1 isdetermined from literature of chemical bonds and valance. In the case ofwater, the angle 19 is approximately 109.5 degrees. In an embodiment,the angle 19 may be between 100 and 115 degrees. FIG. 5 also showsmagnets 5, 9, disposed on second elemental components 3, 7. In this viewmagnets 5, 9, fit into a recessed portion of second elemental components3, 7. However, magnets 5, 9, may also be attached to second elementalcomponents 3, 7, without being in a recessed portion. Magnets 5, 9, maybe attached to second elemental components 3, 7, with a screw, a nail,an adhesive, and the like. By way of example, in an embodiment, magnet 5is attached to second elemental component 3 with an adhesive. In anembodiment, magnet 9 is attached to second elemental component 7 with anadhesive. Magnets of the invention may include any that can display anattractive force, or a repulsive force, great enough for the purposescontemplated herein. In an embodiment, magnets of the invention caninclude ceramic (ferrite), alnico (aluminum, nickel, cobalt), samariumcobalt, neodymium iron boron, and composites. Magnets of the inventioncan be in many different shapes. By way of example, magnets of theinvention can include disk and bar magnets.

Embodiments of the invention can include the use of magnets of differentstrength. By way of example, a primary structural bond can be anattachment between magnets of relatively higher strength while asecondary structural bond can be an attachment between magnets ofrelatively lower strength. By way of example, magnets included in aprimary structural bond can be rare earth magnets such as neodymium ironboron while the magnets included in a secondary structural bond can bealnico. In this manner, the primary structural bonds can have a greaterbonding strength than the secondary structural bonds.

As the magnetic force between to magnets diminishes with increasingdistance, varying bond strength can also be achieved by altering thepositioning of the magnets on the elemental components. By way ofexample, the magnets can be positioned farther below the surface of theelemental components so that the effective distance between magnets isgreater. Referring now to FIG. 6, a cross-sectional schematic view of amodeling component 70 is shown that is similar to that of FIG. 4.However, in this embodiment the magnets are positioned farther away fromthe surface of the elemental component. Specifically, FIG. 6 showsmagnets 11, 13, disposed on first elemental component 1. In this view,magnets 11, 13, are disposed within channels 71 and 73 respectively adistance from the surface of first elemental component 1. In thismanner, the magnets 11, 13 would attach to other magnets less stronglythan they would if they were positioned at the very surface of firstelemental component 1. Magnets 11, 13, may be attached to firstelemental component 1, with a screw, a nail, an adhesive, and the like.By way of example, in an embodiment, magnet 11 is attached to firstelemental component 1 with an adhesive. In an embodiment, magnetscomprising primary structural bonds are disposed closer to the surfaceof the first elemental component than are magnets comprising secondarystructural bonds.

Referring now to FIG. 7, a schematic view of another embodiment of amodeling component 100 in accordance with the invention is shown. Afirst elemental component 101 is shown attached to two second elementalcomponents 103, 107. In this embodiment, first elemental component is acube. Both of the second elemental components 103, 107, have a magnet105, 109, disposed on their surface. Magnets 105, 109, may be attachedwith a screw, a nail, an adhesive, or the like. By way of example,magnet 105 can be attached to second elemental component 103 with anadhesive. The magnets 105, 109, are disposed on second elementalcomponents 103, 107, so as to reflect positions of lesser electrondensity. Magnets 111, 113 are disposed on the surface of first elementalcomponent 101. Magnets 111, 113, may be attached with a screw, a nail,an adhesive, or the like. By way of example, magnet 111 may be attachedto second elemental component 107 with an adhesive.

Embodiments of the present invention may be used to model many differenttypes of molecules that may be hydrogen-bonded either intramolecularlyor to other molecules. By way of example, embodiments of the presentinvention can model ammonia (NH₃) and ammonium ion (NH₄ ⁺), and thehydrogen bonding of these molecules to other molecules. Referring now toFIG. 8, a first elemental component 152, representing nitrogen, isattached to three second elemental components 153, each representing ahydrogen. Together, first elemental component 152 and the three secondelemental components 153 form a complex 151 modeling an ammoniamolecule. Magnets 155 are disposed on each of the three second elementalcomponents 153. Magnets 155 can attach to other magnets (not shown) onother model components to simulate the effects of hydrogen bonding. Amagnet 157 is disposed on the top of first elemental component 152 in aconfiguration to simulate the electron or charge density on a nitrogenatom when it is in an ammonia molecule. Another second elementalcomponent 159 is shown that is not attached to the ammonia complex 151.Second elemental component 159 has magnets 161, 163 disposed on oppositesides, in this view, top and bottom. Magnets 161 and 157 are configuredso that there is an attractive force by which second elemental component159 can attach to first elemental component 152, forming an ammoniumion.

Though embodiments of the invention have been shown in configurationsfor purposes of showing hydrogen bonding for molecules such as water andammonia, one of skill in the art will appreciate that, in embodiments,the invention can also illustrate hydrogen bonding for other atoms andmolecules.

Embodiments of the present invention can be used to model many differentcomplexes. Referring now to FIG. 9, a schematic view of an embodiment ofthe invention modeling a hydrogen-bonded cyclic five-water complex 200is shown. Five first elemental components 201, simulating oxygen atoms,are in a complex held together by five second elemental components 203,simulating hydrogen atoms, that are each attached to one first elementalcomponent in a manner to simulate covalent bonding and attached to onefirst elemental component in a manner to simulate hydrogen bonding. Fivemore second elemental components 205, simulating hydrogen atoms, areeach attached to one first elemental component 201 in a mannersimulating covalent bonding, but are not shown hydrogen bonding toanother component. The non-hydrogen bonded second elemental components205 shown are all pointing up. However, one of skill in the art willappreciate that each one can point either up or down depending on theorientation of the first elemental components 201. In a cyclicfive-water complex, those components simulating oxygen (first elementalcomponents 201) lie approximately in the same plane forming a pentagonalshape when viewed from above or below.

One of skill in the art will appreciate that there are many uses formodels in accordance with the invention. By way of example, models inaccordance with the invention can be used to illustrate and understandtheories regarding the structure and behavior of liquid water. By way ofexample, in quantum mechanics, distinct conformations of pentagonalwater (five-water complex) can be used to represent base states fromwhich another more stable stationary state can be derived, which is atheory that is important to our understanding of liquid water. Further,the mixture theory of liquid water provides that as temperature changes,the concentration of components adjusts following laws ofthermodynamics. By way of example, the pentagonal water conformationwould decrease in concentration with increasing temperature.

Referring now to FIG. 10, a schematic view of an embodiment of theinvention modeling a hydrogen-bonded cyclic six-water complex (primitiveunit cell of hexagonal ice) is shown. Six first elemental components301, simulating oxygen atoms, are in a complex held together by sixsecond elemental components 303, simulating hydrogen atoms, that areeach attached to one first elemental component in a manner to simulatecovalent bonding and attached to one first elemental component in amanner to simulate hydrogen bonding. In a cyclic six-water complex,those components simulating oxygen (first elemental components 301) donot lie flat in the same plane, but rather take on a “puckered”configuration in the plane.

Three second elemental components 305, simulating hydrogen atoms, areeach attached to one first elemental component 301 in a mannersimulating covalent bonding, but are not shown hydrogen bonding toanother component, and are all pointing up. Three more second elementalcomponents 307, simulating hydrogen atoms, are each attached to onefirst elemental component 301 in a manner simulating covalent bonding,and are pointing outward in a radial manner. As visible in thisconfiguration, the model of hexagonal water can simulate lateralhydrogen bonding. Accordingly, as with real hexagonal water, thehexagonal water model structure can fit together with other hexagonalwater models and fit together into a plane.

The hexagonal water model also has a capacity for vertical hydrogenbonding. Referring now to FIG. 11, an offset view of an embodiment ofthe invention modeling a complete unit cell of hexagonal ice is shown.

In an embodiment, the invention can be used to model ion-dipole bonding.Referring now to FIG. 12A, a model of a hydroxyl ion 403 is shown alongwith a model of a water molecule 401. The hydroxyl ion 403 includes afirst elemental component 413 with three secondary structural magnets419 disposed thereon having tetrahedral symmetry (only two of the threeare shown). A second elemental component 415 is attached to the firstelemental component 413 through a primary structural bond (not shown). Aseparate secondary structural magnet 417 is disposed on the secondelemental component 415. Referring now to FIG. 12B, the hydroxyl ion 403and the water molecule 401 can move together in the direction of arrow421 (shown in FIG. 12A) to form the structure of H₃O₂ ⁻, a hydratedhydroxyl molecule 430.

One of skill in the art will appreciate that ion dipole bonding can takeon more complex forms. Referring now to FIG. 13A, the formation of amodel hydronium ion (H₃O⁺) 440 and 450 is shown along with models ofthree water molecules that can hydrate the hydronium ion. A firstelemental component 441 has two magnets 449 (only one shown) disposed onits surface. The first elemental component 441 is attached throughprimary structural bonds to a pair of second elemental components 445.Magnets 447 are disposed on the surface of the second elementalcomponents 445. The first elemental component 441 and the pair of secondelemental components 445 together, in this example, represent a watermolecule 440. A third elemental component 453, in this case representinga hydrogen atom 450, has two magnets 455 disposed on its surface. One ofthe magnets 455 can be attracted to and attach to magnet 449 asindicated by arrow 457. Together, the hydrogen atom 450 and the watermolecule 440 form a hydronium ion that has a net positive charge, sharedequally among the three hydrogen atoms following the theory ofresonance. Three molecular modeling components 401, in this caserepresenting other water molecules, having magnets 409 disposed on theirsurfaces can attach to the exposed magnets 447 and 455 of the newlyformed hydronium ion as indicated by arrows 449, 451, and 452, to form ahydrated hydronium ion (H₉O₄ ⁺) as shown in FIG. 13B. One of skill inthe art will appreciate that many other types of ion-dipole bonds can bemodeled in a like manner using embodiments of the invention.

While not shown in the Figures herein, embodiments of the presentinvention can also be used to model the structure of clathrates (or cagecompound). Clathrates are compounds in which the crystal lattice orstructure of one component (the host molecule) complete encloses spacesin which a second component (the guest molecule) is located. An examplewould be a 20-water complex (H₂O)₂₀ forming a dodecahedron, a cagecompound around guest molecules such as Ar, N₂, O₂, or CO₂. Forming thecage compound from embodiments of the present invention is a simplematter of using components to first create a hydrogen-bonded cyclicfive-water complex such as that shown in FIG. 9 and then arrangingfifteen additional water models into a dodecahedron having a total oftwelve pentagon water structures attached to one another through themagnets contained on their surface, modeling further hydrogen bonding,in order to create the cage compound. There are many examples of waterclathrates reported in the literature containing different guestmolecules and having a variety of host structures, and we expect thepresent invention to be applicable to modeling for all.

While the present invention has been described with reference tospecific poles (North and South) of a magnet pointing in specificdirections, one of skill in the art will recognize that it is therelative orientation of one magnet to another that is significant andnot the absolute orientation of any given magnet. That is, where onecomponent has the North pole of a magnet facing outwardly and isconfigured to interact with another component that has the South pole ofa magnet facing outwardly, the orientation of one magnet can be reversedso long as the orientation of the other magnet, and any other magnetsconfigured for interaction, is also reversed.

While the present invention has been described with reference to severalparticular implementations, those skilled in the art will recognize thatmany changes may be made hereto without departing from the spirit andscope of the present invention.

1. A molecular modeling device comprising: a plurality of molecularcomponents comprising a first elemental component comprising a pluralityof first magnets; a second elemental component comprising a secondmagnet; and a primary structural bond attaching the first elementalcomponent to the second elemental component; wherein molecularcomponents are attached to other molecular components through magneticattraction between first magnets and second magnets; wherein the primarystructural bond attaches more strongly than the secondary structuralbond.
 2. The molecular modeling device of claim 1, the first and secondmagnets each having first and second magnetic poles, the first magnetsdisposed on the exterior of the first elemental component with the firstmagnetic pole pointing away from the interior of the first elementalcomponents; the second magnet disposed on the exterior of the secondelemental component with the second magnetic pole of the second magnetpointing away from the interior of the second elemental component. 3.The molecular modeling device of claim 1, the first magnetic polecomprising a South pole and the second magnetic pole comprising a Northpole.
 4. The molecular modeling device of claim 1, the first magneticpole comprising a North pole and the second magnetic pole comprising aSouth pole.
 5. The molecular modeling device of claim 1, the primarystructural bond non-reversibly attaching the first elemental componentto the second elemental component.
 6. The molecular modeling device ofclaim 1, the primary structural bond comprising a fastening device. 7.The molecular modeling device of claim 3, the fastening devicecomprising a screw.
 8. The molecular modeling device of claim 1, theprimary structural bond comprising an adhesive.
 9. The molecularmodeling device of claim 1, the first elemental component comprising amaterial selected from the group consisting of wood, cellulose fiber,polymer, glass, metal, and a composite.
 10. The molecular modelingdevice of claim 1, the second elemental component comprising a materialselected from the group consisting of wood, cellulose fiber, polymer,glass, metal, and a composite.
 11. The molecular modeling device ofclaim 1, wherein a plurality of molecular components attach to othermolecular components through secondary structural bonds to modelsecondary structure.
 12. The molecular modeling device of claim 1,wherein two second elemental components are non-reversibly attached toone first elemental component.
 13. The molecular modeling device ofclaim 1, wherein the first and second elemental components arespherical.
 14. The molecular modeling device of claim 1, the firstmagnets disposed on the exterior of the first elemental component in anorientation to model the charge symmetry distribution on an atom. 15.The molecular modeling device of claim 1, the first magnets disposed onthe exterior of the first elemental component at a position whereinlines connecting each of the first magnets with the center of the firstelemental component intersect at an angle of between 100 and 115degrees.
 16. The molecular modeling device of claim 15, the anglecomprising a tetrahedral angle of about 109.5 degrees.
 17. A molecularmodeling device comprising: a plurality of molecular componentscomprising a first atomic component and a second atomic component; andmeans for attaching molecular components together to simulate bothprimary and secondary structure of a chemical compound.
 18. Themolecular modeling device of claim 17, wherein the means for attachingmolecular components together to simulate both primary and secondarystructure of a chemical compound simulates both covalent bonding andelectrostatic bonding.
 19. The molecular modeling device of claim 17,wherein the means for attaching molecular components together tosimulate both primary and secondary structure of a chemical compoundsimulates both covalent bonding and hydrogen bonding.